---
title: "Statistical Significance of a Pairwise Alignment of Sequences"
author: "Alex-Alex-Helena"
date: "10.11.2021"
output: 
  flexdashboard::flex_dashboard:
    orientation: rows
    social: menu
    source_code: embed
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(StatSignfPairSeqAlign)
```

Simple Example
====================================================================================================================================

### Output {data-width=450}

```{r}
seq1 <- ">random sequence 1 consisting of 20 residues.
KMMIDIHWGMWWYEYMMCLD"

seq2 <- ">random sequence 1 consisting of 20 residues.
DVYRVCQNVFRYHHFCKRTI"

out <- statSignf(seq1, seq2)
```

### Plot {data-width=550}

```{r}
out()
```

Local Alignment
====================================================================================================================================

### Output {data-width=450}

```{r}
seq1 <- ">random sequence 1 consisting of 20 residues.
KMMIDIHWGMWWYEYMMCLD"

seq2 <- ">random sequence 1 consisting of 20 residues.
DVYRVCQNVFRYHHFCKRTI"

out <- statSignf(seq1, seq2, num.shuffles = 3000,
      subst.matrix = "BLOSUM45", kind.align = "local")
```

### Plot {data-width=550}

```{r}
out()
```

Non-random Sequences
====================================================================================================================================

### Output {data-width=450}

```{r}
seq1 <- ">non-random sequence 1 very similar to 2.
KKKKKKKKKKRRRRNNRRLLLMMMNM"

seq2 <- ">non-random sequence 2 very similar to 1.
KKKKKKKKKKKRRRRRRLLLLMMMNN"

out <- statSignf(seq1, seq2, num.shuffles = 2000,
      subst.matrix = "BLOSUM100", shuffle.seq = 2, gap.scores = c(8, 2))
```

### Plot {data-width=550}

```{r}
out()
```


Longer Sequences
====================================================================================================================================

Column {.sidebar data-width=700}
-------------------------------------
### Output
```{r}
out <- statSignf(seq1, seq2,
      subst.matrix = "PAM250", kind.align = "local")
```

Row {data-height=310}
-------------------------------------
### Sequence 1
```{r}
seq1 <- ">random sequence 1 consisting of 500 residues.
YWWCSKEWDHFPDVTTCTPSEQYPAWAMHNMILPNWQLAEMMQSYRYIPNIALPNHQLTK
AHSMWAQHSMYVQRCCETKDLLFNDDTSQDKAYPFKQMESNHHITNEFPNKCKILTSVKH
ATLWNLQALGCCKDPCRSNKFHKKLNIDIHCSPGWTGWNAQYSSPGPFCWEPKTVNYSWF
RFKWHYFPCVHNIGSSRQCVWLRYFHLSSEQWKQGARGWVVVIFGACSGWYPWDNGQLYQ
EKNIFCAGKGQCATDQYFNYLWSWMISAGWAVYPYDECVTRTVISLFEVAYYFRHPYMWH
NITIMLRNETLPAVTQCVLETLHTHYCLALWLEEMYPCTDEGYNRKTPGDTHVQDCAFFS
ESHKHDVKTNWVGSDSINYNPGSVMWKICDHLGAGMYGRPTPADWSQSIITNHICCGDAS
HCGEQWCAVNNDSVSTMISQFQTSEWAHPIVINQHGIEPDMSWGELARVLTQNPGLGQQN
TIRMKTFYRKFFPCMYFNFQ"
```

### Sequence 2
```{r}
seq2 <- ">random sequence 1 consisting of 500 residues.
FWMLVNRLCQDTGWEYADCRPDHGNESRMMYKDCFYHITDPAEATVFPIESFCQHLCSNF
WSNTHWRIINYPPLHWKNYCGSAFWGRNYGEWSCFEDRMPFATEIETHSNPVFNDFQEAQ
CNNQARKKNGWKVSAPQEAMPQGMMRLTWIFIHEMWGWFSWVWRLIQNQINEPGVKPLEL
CSETQHGVFGWRDIAIMIRMEYKCDVLFMWLILCPCYYSDQFCKRIAAHQEAMRWKIAKT
AWQFVGKIKGPKCRMLTERRQFACEVTEQACKRCLPHAVRHTGQSHKYHCTAFRPFTKIS
VAYGVEIGESFFFQWYWQFRFSFATAWAISNWGQGWSLCIEEVNWNDIKEHFTFTTKIML
VFTENFTEHSQEIFDSLMDHGPDHKVSIIARQMVACQIWITHKMGCCHDGLLYTPTHDWF
LQVRVPCFFQWVEGWNGIEDDIPGHVRMNSMTSWLNKPLASRILLDIYIMTWDNRWFKWD
KTWMVVGHNIHDAWSFENVK"
```   

Row {data-height=690}
-------------------------------------
### Plot
```{r}
out()
```

DNA
====================================================================================================================================

Column {.sidebar data-width=650}
-------------------------------------
### Output
```{r}
out <- statSignf(seq1, seq2, kind.seq = "DNA", gap.scores = c(8, 2), 
                 num.shuffles = 200)
```

Row {data-height=450}
-------------------------------------
### Sequence 1
```{r}
seq1 <- ">random sequence 1 consisting of 800 bases.
ctattggccgttggaggggaagtgtatcgactcgtcaagcgctctaatgagaaaccggct
tactcgccctcttatgatccttgacaagcgtctgactccgcaaggatcccgggctgaggg
ctacacccacctcgtttttagttttttaacagcagaaatcagcccgacgaagaacgagga
aggttctattaagagccgacggatccgaagaacacgtggtccctgacccttagaaccgat
tcgcgggctaaaaagcaacacgcttcgacccgatctgtcgcattgaattgaaacgcccct
ttattgtagctactaaccaggcttccttatagctattagcagggctggaagtgcggattc
actctaagacggtcacagctcatcagctcccctgcctgtagctgaacgtaccaatatctg
caagtaacaaccttgagtaccgtaagactgtaaaaatcttcgattccgcattatagggca
aggctaacgcatttccgccaaaggagaatgaggttgttgcattcccgtgagtgaaaggtc
ttagaaaacaagttcgatgcgcaggaggttcagattctgttccccccgtcgcgccgcgcc
tcaaaacccggtaccttcgcaaggagcccccagactctatggctaatcacttgtttgcaa
gaggctctgatccaaatgacatcaacctaacgcacaaagctgaccgaatataaacgattt
tctagcatatcgcgttttaattcgctagctgcagctttcgcatccgtcgccgctttaggc
ggggcgaacatcctgacccg"
```

### Sequence 2
```{r}
seq2 <- ">random sequence 1 consisting of 800 bases.
gagtgttttcattagcatccgcttagcatgggggtatgctgtactagtagacgtcagaga
taaggactggtcataattcaaggcgccgccatactaatgttagccttgttaatgactaat
aaatcctccccggaaatccataacaacgaagcctcgcgattacccgcaacgagaaaaact
caataaagggaaggcagacaaatgtatgcagatagtgcatgttctgcgaacactccacgt
atttgaacatataatcctaaaggtgtgttacccgagacactccgtccactctcgtcggta
acataagggtcgtcttttagtaacttccagcggtcatactaacaggctcatcgcactggt
agattctgtgcgggtaaacgcattatagacttgtgtcgagcccccggtgctggcgaattg
tccgcaggggcgacaggagtcaaaacgtgcttgaacaagaccgaacctatgtccttctga
gacgggatctccaatcgccccactgcggagcccctggcaccgcttatgccctagcagtca
ctgtacaaaacctatagccgtgccaccactcagcccgtctacggctgcaccgctactcaa
gtcccgagactcacgctgctcgaactgccttactctggtcaatagagcttaggaacctgt
gtaacggcatgcgttctgtgttagttaaatcgtgacatggcgcccaagcacagtcataat
tattgaaagttatctacatgggatgatgagcactgagggacgcaccgcgcctttatccat
ctatgccgcggcccgttcca"
```   

Row {data-height=550}
-------------------------------------
### Plot
```{r}
out()
```

Suppress Output and Plotting
====================================================================================================================================

### Output {data-width=500}

```{r}
seq1 <- ">random sequence 1 consisting of 20 residues.
KMMIDIHWGMWWYEYMMCLD"

seq2 <- ">random sequence 1 consisting of 20 residues.
DVYRVCQNVFRYHHFCKRTI"

out <- statSignf(seq1, seq2,
       plot = F, suppress.output = T)
```

### Plot {data-width=500}

```{r}
# out() gives an error, since 'out' is no longer a function. 
out
```